When working with periodic boundary conditions it often happens that a molecule may pass from one side of the box to the other.
When using MDTraj you can use the command image_molecules to make sure that some selected molecules stay within the box throughout the trajectory.
Does TTClust offer the possibility of performing such a step or does it in any way account for PBC during RMSD calculations?
It's very easy to just preprocess the trajectory, but it would ease the process to have the software directly perform this action.
When working with periodic boundary conditions it often happens that a molecule may pass from one side of the box to the other. When using MDTraj you can use the command image_molecules to make sure that some selected molecules stay within the box throughout the trajectory. Does TTClust offer the possibility of performing such a step or does it in any way account for PBC during RMSD calculations? It's very easy to just preprocess the trajectory, but it would ease the process to have the software directly perform this action.